If you compare the 40rnder to your other mags, look at the back locking tab. Is the distance between the top edge of the feed lips and the BOTTOM edge of the locking tab different? I'm thinking that maybe because of the position of the locking tab, the mag sticks too far into the mag well, which could result in the bolt getting hung up on the lips or the edge of the feed 'mouth'. Also check to see if your bolt locking lever is engaged when you have this problem.
You know how the rounds are staggered side-to-side when you load them into a clip? Look to see whether the top round is on the left or right when this happens. The bolt may be getting hung up on that top round.
Troubleshooting it might be simple once we have a good list of symptoms.